A friend just asked me, "I had a EU question for ya. THe last few novels that I have read have alluded to Luke going to the dark side with the clone emperor. I have other people talk about it too. Is that right? If so, where do I find that story line? I don't know if they are in a comic series or novel series."

The events you describe happen in Dark Empire and Dark Empire II, and possibly Empire's End, comics that came out in the mid-90s. You can even find a few action figures from these stories, part of the EU line in 1998.

I'm not sure how well they'll match up with the current clone ideas, but back then I thought they were great. Some people really didn't like it, but I found it interesting to see Luke delve into the dark side to infiltrate the Clone Emperor's defenses. I remember him slowly getting cocky and arrogant as he began to lose control of himself. Some of these themes were later revisited in the back story of Mace Windu as his fighting style is based on partially giving himself over to darker feelings.

One concept I always loved about this storyline was the notion that the Emperor is filled with some much hateful power that his body literally deteriotes and he needs back-up bodies in the form of clones. This always explained to me why The Emperor in ESB looks (looked) so different than he does in RotJ.